Catalina Vallejos
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BASiCS |
| git_branch: RELEASE_3_18 |
| git_last_commit: 7b60c29 |
| git_last_commit_date: 2024-03-11 13:42:52 -0400 (Mon, 11 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:31 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 129/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCS 2.14.0 (landing page) Catalina Vallejos
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BASiCS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BASiCS |
| Version: 2.14.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BASiCS_2.14.0.tar.gz |
| StartedAt: 2024-03-27 23:30:53 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 23:53:53 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 1379.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BASiCS_2.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BASiCS’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BASiCS_TestDE 18.563 0.179 20.695
BASiCS_MCMC 16.821 0.279 18.486
BASiCS_PlotDE 9.473 0.089 10.517
newBASiCS_Chain 8.258 0.133 8.895
BASiCS_Chain 7.704 0.116 8.328
BASiCS_DenoisedCounts 4.848 0.037 5.334
BASiCS_Chain-methods 4.716 0.141 5.512
BASiCS_DivideAndConquer 4.756 0.094 59.454
BASiCS_DiagPlot 4.739 0.038 5.415
BASiCS_DenoisedRates 4.605 0.036 5.072
BASiCS_Summary 4.349 0.083 5.115
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/00check.log’
for details.
BASiCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BASiCS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘BASiCS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BASiCS.cpp -o BASiCS.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BASiCS.so BASiCS.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-BASiCS/00new/BASiCS/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BASiCS)
BASiCS.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(BASiCS)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
Bioconductor, please visit:
https://github.com/catavallejos/BASiCS/wiki.
>
> test_check("BASiCS")
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
-------------------------------------------------------------
For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
EFDR calibration failed for Differential mean task.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
For Differential residual dispersion task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdR'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
EFDR calibration failed for Differential mean task.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
For Differential residual dispersion task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdR'.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.017
system: 0
elapsed: 0.019
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.017
system: 0
elapsed: 0.018
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.016
system: 0
elapsed: 0.018
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.019
system: 0
elapsed: 0.022
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.015
system: 0.001
elapsed: 0.02
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.015
system: 0
elapsed: 0.016
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.014
system: 0
elapsed: 0.016
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.015
system: 0
elapsed: 0.015
-------------------------------------------------------------
Output
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.012
system: 0
elapsed: 0.014
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.015
system: 0.001
elapsed: 0.02
-------------------------------------------------------------
Output
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.019
system: 0.001
elapsed: 0.023
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.017
system: 0
elapsed: 0.021
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.013
system: 0
elapsed: 0.014
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.017
system: 0.001
elapsed: 0.019
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.017
system: 0
elapsed: 0.018
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.015
system: 0.001
elapsed: 0.015
-------------------------------------------------------------
Output
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.015
system: 0.001
elapsed: 0.016
-------------------------------------------------------------
Output
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.024
system: 0
elapsed: 0.027
-------------------------------------------------------------
Output
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.106
system: 0.001
elapsed: 0.124
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.113
system: 0.001
elapsed: 0.123
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Combining batch posteriors for beta
Combining batch posteriors for sigma2
Combining batch posteriors for epsilon
Combining batch posteriors for RBFLocations
Combining batch posteriors for mu
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for phi
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
Cannot find a balanced split with 9 quantiles, trying again with 8
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.117
system: 0.001
elapsed: 0.136
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.101
system: 0.001
elapsed: 0.114
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
Generating partitions...
Starting MCMC...
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-----------------------------------------------------
MCMC sampler has been started: 200 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
All 200 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
Minimum acceptance rate among mu[i]'s: 0.2
Average acceptance rate among mu[i]'s: 0.4968
Maximum acceptance rate among mu[i]'s: 0.77
Minimum acceptance rate among delta[i]'s: 0.54
Average acceptance rate among delta[i]'s: 0.6786
Maximum acceptance rate among delta[i]'s: 0.83
Minimum acceptance rate among nu[jk]'s: 0.79
Average acceptance rate among nu[jk]'s: 0.9498
Maximum acceptance rate among nu[jk]'s: 1
Minimum acceptance rate among theta[k]'s: 1
Average acceptance rate among theta[k]'s: 1
Maximum acceptance rate among theta[k]'s: 1
-----------------------------------------------------
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.309
system: 0.003
elapsed: 0.374
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-----------------------------------------------------
MCMC sampler has been started: 200 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
All 200 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
Minimum acceptance rate among mu[i]'s: 0.17
Average acceptance rate among mu[i]'s: 0.5022
Maximum acceptance rate among mu[i]'s: 0.84
Minimum acceptance rate among delta[i]'s: 0.54
Average acceptance rate among delta[i]'s: 0.68
Maximum acceptance rate among delta[i]'s: 0.82
Minimum acceptance rate among nu[jk]'s: 0.84
Average acceptance rate among nu[jk]'s: 0.9607
Maximum acceptance rate among nu[jk]'s: 1
Minimum acceptance rate among theta[k]'s: 0
Average acceptance rate among theta[k]'s: 0.48
Maximum acceptance rate among theta[k]'s: 0.96
-----------------------------------------------------
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.299
system: 0.002
elapsed: 0.319
-------------------------------------------------------------
Output
-------------------------------------------------------------
Combining batch posteriors for mu
Combining batch posteriors for delta
Combining batch posteriors for s
Combining batch posteriors for nu
Combining batch posteriors for theta
For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
Evaluating variance contribution threshold = 25 % ...
Evaluating variance contribution threshold = 50 % ...
Evaluating variance contribution threshold = 75 % ...
Evaluating variance contribution threshold = 25 % ...
Evaluating variance contribution threshold = 50 % ...
Evaluating variance contribution threshold = 75 % ...
For LVG detection task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThreshold'.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.009
system: 0
elapsed: 0.009
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.009
system: 0
elapsed: 0.009
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.017
system: 0
elapsed: 0.018
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.01
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.007
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.01
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.007
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006
-------------------------------------------------------------
Output
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.007
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.011
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.01
system: 0
elapsed: 0.011
-------------------------------------------------------------
Output
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.006
system: 0
elapsed: 0.006
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.009
system: 0
elapsed: 0.009
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.009
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.012
system: 0
elapsed: 0.012
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.016
system: 0
elapsed: 0.017
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.011
system: 0
elapsed: 0.013
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 : horizontal integration (no-spikes case)
-------------------------------------------------------------
Randomly, 1 out of 10
genes was left as reference at each iteration
List of reference genes and frequencies stored as a .txt file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.015
system: 0
elapsed: 0.015
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS_Chain object stored as chain_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 : horizontal integration (no-spikes case)
-------------------------------------------------------------
Randomly, 1 out of 10
genes was left as reference at each iteration
List of reference genes and frequencies stored as a .txt file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.013
system: 0.001
elapsed: 0.015
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
`BASiCS_Chain` class definition was outdated.
Object updated to be compatible with BASiCS version 2.14.0.
Set 'StoreUpdatedChain' = TRUE to save updated object.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.013
system: 0
elapsed: 0.012
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
`BASiCS_Chain` class definition was outdated.
Object updated to be compatible with BASiCS version 2.14.0.
Set 'StoreUpdatedChain' = TRUE to save updated object.
(this overwrites original input file).
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 1
(ratio Group1 vs Group2).
-------------------------------------------------------------
EFDR calibration failed for Differential mean task.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
EFDR calibration failed for Differential residual dispersion task.
Probability threshold automatically set equal to 'ProbThresholdR'.
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.035
system: 0
elapsed: 0.043
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 1
(ratio Group1 vs Group2).
-------------------------------------------------------------
EFDR calibration failed for Differential mean task.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
EFDR calibration failed for Differential residual dispersion task.
Probability threshold automatically set equal to 'ProbThresholdR'.
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.578
system: 0.003
elapsed: 0.61
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.005
system: 0
elapsed: 0.006
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.575
system: 0.002
elapsed: 0.586
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.516
system: 0.003
elapsed: 0.541
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.518
system: 0.005
elapsed: 0.59
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.005
system: 0
elapsed: 0.004
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.492
system: 0.003
elapsed: 0.547
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.487
system: 0.003
elapsed: 0.514
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.69
system: 0.005
elapsed: 0.72
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.692
system: 0.005
elapsed: 0.711
-------------------------------------------------------------
Output
-------------------------------------------------------------
Running no spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.034
system: 0
elapsed: 0.035
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.767
system: 0.005
elapsed: 0.885
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.007
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in
'/Users/biocbuild/bbs-3.18-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ...
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
EFDR calibration failed for Differential mean task.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
For Differential residual dispersion task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdR'.
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.009
system: 0
elapsed: 0.011
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.009
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
Running with spikes BASiCS sampler (regression case) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.008
system: 0
elapsed: 0.008
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
'BatchInfo' was treated as a factor with 2 levels:
1 2
'BatchInfo' was treated as a factor with 2 levels:
1 2
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running no spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.005
system: 0
elapsed: 0.006
-------------------------------------------------------------
Output
-------------------------------------------------------------
'BatchInfo' was treated as a factor with 2 levels:
1 2
altExp 'spike-ins' is assumed to contain spike-in genes.
see help(altExp) for details.
-------------------------------------------------------------
NOTE: default choice PriorDelta = 'log-normal' (recommended value).
Vallejos et al (2015) used a 'gamma' prior instead.
-------------------------------------------------------------
Running with spikes BASiCS sampler (no regression) ...
-------------------------------------------------------------
MCMC running time
-------------------------------------------------------------
user: 0.007
system: 0
elapsed: 0.006
-------------------------------------------------------------
Output
-------------------------------------------------------------
-------------------------------------------------------------
BASiCS version 2.14.0 :
vertical integration (spikes case)
-------------------------------------------------------------
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 459 ]
>
> proc.time()
user system elapsed
496.174 9.937 654.193
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 4.716 | 0.141 | 5.512 | |
| BASiCS_Chain | 7.704 | 0.116 | 8.328 | |
| BASiCS_CorrectOffset | 0.022 | 0.009 | 0.038 | |
| BASiCS_DenoisedCounts | 4.848 | 0.037 | 5.334 | |
| BASiCS_DenoisedRates | 4.605 | 0.036 | 5.072 | |
| BASiCS_DetectVG | 1.800 | 0.147 | 2.159 | |
| BASiCS_DiagHist | 2.261 | 0.048 | 2.455 | |
| BASiCS_DiagPlot | 4.739 | 0.038 | 5.415 | |
| BASiCS_DivideAndConquer | 4.756 | 0.094 | 59.454 | |
| BASiCS_Draw | 0.936 | 0.020 | 1.023 | |
| BASiCS_EffectiveSize | 0.466 | 0.019 | 0.535 | |
| BASiCS_Filter | 0.003 | 0.001 | 0.005 | |
| BASiCS_LoadChain | 4.190 | 0.108 | 4.692 | |
| BASiCS_MCMC | 16.821 | 0.279 | 18.486 | |
| BASiCS_MockSCE | 0.912 | 0.007 | 1.003 | |
| BASiCS_PlotDE | 9.473 | 0.089 | 10.517 | |
| BASiCS_PlotOffset | 2.601 | 0.027 | 3.034 | |
| BASiCS_PlotVG | 0.930 | 0.023 | 1.118 | |
| BASiCS_PriorParam | 0.709 | 0.012 | 0.843 | |
| BASiCS_ShowFit | 1.007 | 0.018 | 1.211 | |
| BASiCS_Sim | 1.979 | 0.018 | 2.378 | |
| BASiCS_Summary-methods | 0.008 | 0.004 | 0.013 | |
| BASiCS_Summary | 4.349 | 0.083 | 5.115 | |
| BASiCS_TestDE | 18.563 | 0.179 | 20.695 | |
| BASiCS_VarThresholdSearchHVG_LVG | 4.479 | 0.133 | 4.952 | |
| BASiCS_VarianceDecomp | 0.558 | 0.012 | 0.604 | |
| Summary-BASiCS_Chain-method | 0.449 | 0.006 | 0.476 | |
| dim-BASiCS_Chain-method | 0.010 | 0.015 | 0.026 | |
| dimnames-BASiCS_Chain-method | 0.010 | 0.015 | 0.025 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.256 | 0.103 | 0.690 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.235 | 0.057 | 0.344 | |
| makeExampleBASiCS_Data | 0.702 | 0.005 | 0.755 | |
| newBASiCS_Chain | 8.258 | 0.133 | 8.895 | |
| plot-BASiCS_Chain-method | 0.241 | 0.060 | 0.332 | |
| plot-BASiCS_Summary-method | 0.241 | 0.058 | 0.543 | |
| show-BASiCS_ResultDE-method | 0.236 | 0.058 | 0.310 | |
| show-BASiCS_ResultVG-method | 0.237 | 0.058 | 0.313 | |
| show-BASiCS_ResultsDE-method | 0.240 | 0.058 | 0.328 | |
| subset-BASiCS_Chain-method | 2.047 | 0.019 | 2.278 | |